DNA methylation in bacteria occurs in diverse sequence contexts and plays significant functional roles in cellular defense and gene regulation.
Three different forms of DNA methylation exist in bacterial genomes: N6-methyladenine (6mA), which is the most prevalent form; N4-methylcytosine (4mC); and 5-methylcytosine (5mC). Because bacteria lack histones and nucleosomes, DNA methylation is their primary means of epigenetic gene regulation.
Several studies have reported that bacterial DNA methylation has important roles affecting clinically relevant phenotypes such as virulence, host colonization, sporulation, biofilm formation, among others.
Nanopore sequencing, or “Strand sequencing,” provides an excellent opportunity for direct detection of chemical DNA modification. Nanopore sequencing has the additional potential to detect epigenetic modifications such as 5-methylcytosine and 5-hydroxymethylcytosine as well as abasic sites.
DNA sequencing is an effective method to reveal genetic variations at the molecular level and in understanding genome-wide methylation with single-nucleotide resolution. However, current methods and technologies used to detect DNA modifications from nanopore sequencing data do not effectively support the de novo study of unknown bacterial methylomes.
Read the original publication of this study here: [ Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing ]
This study aimed to effectively capture the complex nanopore sequencing signal through a method that couples the identification and fine mapping of the three forms of DNA methylation into a multi-label classification design.
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Discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiome using nanopore sequencing
Researchers observed that nanopore sequencing signal displays complex heterogeneity across methylation events of the same type by examining three types of DNA methylation in a large diversity of sequence contexts.
In this study, nanodisco, a training dataset, was generated from an assortment of bacterial species to enable nanopore sequencing for broadly applicable methylation discovery. This method couples the identification and fine mapping of the three methylation forms into a multi-label classification framework.
Nanodisco dataset was applied to a single bacteria and the mouse gut microbiome for reliable methylation discovery.
In the microbiome analysis, the researchers demonstrated identifying misassembled metagenomic contigs (overlapping DNA segments from environmental samples). In addition, the microbiome analysis and the use of DNA methylation for binning metagenomic contigs and associating mobile genetic elements with their host genomes were also shown.
This technology has broad utility for discovering different forms of DNA methylation from bacteria, assisting functional studies of epigenetic regulation in bacteria, and exploiting bacterial epigenomes for more effective metagenomic analyses.
Furthermore, this novel method helps researchers discover DNA methylation from bacterial pathogens more effectively, opening new opportunities for approaching bacterial pathogens and antibiotics resistance.
- A more substantial study of bacterial DNA methylation requires reliable technologies. Nanodisco fills an important gap in that it now enables the use of Nanopore sequencing to make discoveries from bacterial genomes.
- DNA methylation in bacteria occurs in diverse sequence contexts and plays significant functional roles in cellular defense and gene regulation.
- DNA methylation is also prevalent in bacteria, but our current understanding is still at a relatively early stage.
You can read the original publication of this study here: [ Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing ]
- Deciphering bacterial epigenomes using modern sequencing technologies
- Epigenetic Gene Regulation in the Bacterial World
- Advances in Genetics